well this is embarrassing...

[natalie]

how exactly do you use fertilizer in the game to breed flowers..

 

[Mayor o' Pawville]

All you have to do is keep it buried next to the flowers you want to breed. It doesn't guarantee that you will get a hybrid, but it will help greatly.

 

[FraudulentDimetrodon]

Dig a hole next to the flowers you wish to fertilize (the hole tile must be touching the tiles with the flowers), then just bury the Fertilizer. I believe you have optimal results if you bury the Fertilizer with a Golden Shovel, but just using Fertilizer should help some!

The way I plot them is in a diamond formation with the Fertilizer in the middle.

 

[Libertae]

All you have to do is keep it buried next to the flowers you want to breed. It doesn't guarantee that you will get a hybrid, but it will help greatly.

Pretty much this. Everything that surrounds the fertilizer when buried has an increased chance of breeding to make a new hybrid.